[gmx-users] MD Error after adding a unnatural amio acid

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jan 25 11:06:52 CET 2007

Hi Liu Yuemin,

>Minimizations could not had been done if
> building block is a problem, right?

To start with that: it may well be. Energy minimization just tries to
find the nearest well of the energy landscape, relieving most strain.
But in some cases there will still be strain, especially when trying
to combine different parts manually, rather than starting from a
complete (crystal) structure.

> I am trying to build a protein with a non-standard
> amino acid by adding (covalent bond, this is what I
> mean by linkage )

Okay, I did get that.., but read
http://catb.org/esr/faqs/smart-questions.html to get a bit of the idea
about repliers attitude ;)

> a bulky group (163 atoms) to the
> side chain of an existing natural amino acid of wild
> type protein.

Maybe it helps if you're more specific on that. Is this a cofactor?
What is it? Does it contain phosphate/sulphate?

> Energy minimization of the modified
> protein had been performed in gas phase and solvent.
> The solvent and whole system were also minimized and
> equilibrated at different temperatures before MD
> simulation.

What was the final maximum force and on which atom? What was the final
potential energy?

> During MD, either the covalent I build or
> its neighboring one got broken, and the simulation
> terminated.

Have you tried a simulation of the added part or that part attached to
a single amino acid to check its stability in simulation?

> Minimizations could not had been done if
> building block is a problem, right?

> Following is the
> line in my mdp file:
> tc-grps                  = Protein_A ASO_A ASO_B SOL

If the answer there is yes, I won't reply any more until you've read
the posts in the archive you get after a search of the mailing lists
(@ www.gromacs.org) regarding "ref_t tau_t" and possibly my first name
(to make it easier on you). This also goes for the separate coupling
of NA and CL.


Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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